[yt-users] DM density profiles

[Matthew Turk]

Hi Junhwan,

On Wed, Jan 20, 2016 at 12:23 PM, Junhwan Choi (최준환) <choi.junhwan at gmail.com
> wrote:

> Please read below after you comments:
>
> On Tue, Jan 19, 2016 at 2:25 PM, Matthew Turk <matthewturk at gmail.com>
> wrote:
> > Hi Junhwan,
> >
> > On Tue, Jan 19, 2016 at 12:43 PM, Junhwan Choi (최준환)
> > <choi.junhwan at gmail.com> wrote:
> >>
> >> Hi yt user,
> >>
> >> I make a simple DM and gas density profile for my enzo simulation with
> >> following script:
> >> ======================
> >> import matplotlib as matplotlib
> >> matplotlib.use('Agg')
> >> import yt
> >> import yt.units as units
> >> import numpy as np
> >> import matplotlib.pyplot as plt
> >>
> >> def _radiuspc(field, data):
> >>     return data[('radius')].in_units('pc')
> >> yt.add_field('radiuspc', function=_radiuspc, units="pc")
> >>
> >> Nbin= 100
> >> rmax = 4000
> >> index = 60
> >> ds = yt.load("../DD%04d/DD%04d" % (index,index))
> >> ds.index
> >> ad= ds.all_data()
> >>
> >> center = ds.find_max(("gas", "density"))[1]
> >> my_sphere = ds.sphere(center, rmax*units.pc)
> >>
> >> rmin = max([1.0e-4,2.0*ds.index.get_smallest_dx().in_units('pc')])
> >> profile = yt.Profile1D(my_sphere, 'radiuspc', Nbin, x_min=rmin,
> >> x_max=rmax, x_log=True, weight_field='cell_volume')
> >> profile.add_fields(('gas','density'))
> >> profile.add_fields(('gas','dark_matter_density'))
> >> profile.add_fields(('deposit','all_density'))
> >>
> >> plt.plot(np.log10(profile.x), np.log10(profile[('gas','density')]),
> >> label="('gas','density')", linestyle="-", color='g')
> >> plt.plot(np.log10(profile.x),
> >> np.log10(profile[('gas','dark_matter_density')]),
> >> label="('gas','dark_matter_density')", linestyle="-", color='r')
> >> plt.plot(np.log10(profile.x),
> >> np.log10(profile[('deposit','all_density')]),
> >> label="('deposit','all_density')", linestyle="-", color='b')
> >>
> >> plt.legend(loc=0,prop={'size':9})
> >> plt.savefig('DMTest')
> >> ======================
> >>
> >> The only particle in the simulation is the dark matter so that
> >> profile[('gas','dark_matter_density')] and
> >> profile[('deposit','all_density')] should be same.
> >> However, as shown in the attached figure, they are very different.
> >> I would like to ask a few questions regarding to this plot.
> >> 1) Why do profile[('gas','dark_matter_density')] and
> >>
> >> profile[('deposit','all_density')] show significant difference?
> >
> >
> > I can't say for sure, but note that in many areas they do agree.  They're
> > generated differently; one comes from Enzo, one from yt.  Where they
> > disagree, I would suspect there is lacking data.
> >
> >>
> >> 2) What limit the minimum r in profile[('deposit','all_density')]?
> >
> >
> > Probably the grid size, or the cell size at which there're particles.
> >
> Is there any document to control the deposit fields?
> There are 2+1 issues maybe regarding the deposit fields:
> 1) "rmin" in the figure for profile[('deposit','all_density')],
> smallest r with non-zero profile[('deposit','all_density')],
> is 100 times larger than smallest grid-size for the particle force
> resolution and several order larger than minimum
> AMR of the output (see gas density profile). It looks like there is a
> parameter control the rmin of the profile[('deposit','all_density')].
>

Yes, this sounds likely.


> 2) When I try to make the same profile with output which maximum ARM
> is high, the script crash with memory error.
>

This shouldn't happen.  I don't know why.


> For test I change ('deposit','all_density') to
> ('gas','dark_matter_density'), the code work fine, with incorrect
> value.
> I would like to get rid of this memory error. To do so, I need
> understand how deposit field work.
>

For grids, it's quite simple -- the particles simply get deposited into
empty grids.  It shouldn't take any more memory than if you're depositing
gas.  What happens if you try to deposit a *bunch* of grid fields?


> 3) Is there any accumulation method when I use yt.Profile1D?
>
>
No, you have to manually do that, I believe.  I thought we added the
ability to do that in the constructor but I don't see it now.


>
> >>
> >> 3) If I would like to make total density profile, what do I do?
> >>     I think that profile[('deposit','all_density')] is more liable
> result.
> >>     Can I add data[('gas','density')] and
> >> data[('deposit','all_density')], two different field types, in the
> >> derived field?
> >
> >
> > Yes, those two can be added.
> >
> Thank you, it works!!!
>
> >>
> >>
> >> Thank you in advance,
> >> Junhwan Choi
> >>
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> >>
> >
> >
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